[English] 日本語
Yorodumi
- PDB-5b3v: Crystal structure of biliverdin reductase in complex with biliver... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5b3v
TitleCrystal structure of biliverdin reductase in complex with biliverdin and NADP+ from Synechocystis sp. PCC 6803
ComponentsBiliverdin reductase
KeywordsTRANSFERASE / biliverdin reductase / heme degrading pathway / NAD(P)H-dependent enzyme / tetrapyrrole / Rossmann fold
Function / homologyGfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / NAD(P)-binding domain superfamily / nucleotide binding / BILIVERDINE IX ALPHA / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Biliverdin reductase
Function and homology information
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.594 Å
AuthorsTakao, H. / Wada, K.
Citation
Journal: Nat Commun / Year: 2017
Title: A substrate-bound structure of cyanobacterial biliverdin reductase identifies stacked substrates as critical for activity
Authors: Takao, H. / Hirabayashi, K. / Nishigaya, Y. / Kouriki, H. / Nakaniwa, T. / Hagiwara, Y. / Harada, J. / Sato, H. / Yamazaki, T. / Sakakibara, Y. / Suiko, M. / Asada, Y. / Takahashi, Y. / ...Authors: Takao, H. / Hirabayashi, K. / Nishigaya, Y. / Kouriki, H. / Nakaniwa, T. / Hagiwara, Y. / Harada, J. / Sato, H. / Yamazaki, T. / Sakakibara, Y. / Suiko, M. / Asada, Y. / Takahashi, Y. / Yamamoto, K. / Fukuyama, K. / Sugishima, M. / Wada, K.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2011
Title: Expression, purification and preliminary X-ray crystallographic analysis of cyanobacterial biliverdin reductase.
Authors: Watanabe, A. / Hirata, K. / Hagiwara, Y. / Yutani, Y. / Sugishima, M. / Yamamoto, M. / Fukuyama, K. / Wada, K.
History
DepositionMar 13, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Aug 11, 2021Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Biliverdin reductase
A: Biliverdin reductase
C: Biliverdin reductase
D: Biliverdin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,49016
Polymers147,8554
Non-polymers7,63512
Water4,089227
1
B: Biliverdin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8724
Polymers36,9641
Non-polymers1,9093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Biliverdin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8724
Polymers36,9641
Non-polymers1,9093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Biliverdin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8724
Polymers36,9641
Non-polymers1,9093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Biliverdin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8724
Polymers36,9641
Non-polymers1,9093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.500, 100.413, 138.028
Angle α, β, γ (deg.)90.00, 95.53, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Biliverdin reductase /


Mass: 36963.770 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Kazusa / Gene: bvdR / Production host: Escherichia coli (E. coli) / References: UniProt: P72782
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C33H34N4O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG4000, Trizma (pH8.2), magnesium chloride, barium chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 8, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.594→50 Å / Num. obs: 46736 / % possible obs: 99.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 7.4
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 19.83 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
PHENIXphasing
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B3T

5b3t


Resolution: 2.594→49.624 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2576 2216 4.77 %
Rwork0.208 --
obs0.2103 46428 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.594→49.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9993 0 536 227 10756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510789
X-RAY DIFFRACTIONf_angle_d1.76114703
X-RAY DIFFRACTIONf_dihedral_angle_d15.2946191
X-RAY DIFFRACTIONf_chiral_restr0.0731557
X-RAY DIFFRACTIONf_plane_restr0.0041877
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.594-2.65040.36341270.26952506X-RAY DIFFRACTION89
2.6504-2.7120.29471440.26162697X-RAY DIFFRACTION98
2.712-2.77980.30341400.2612783X-RAY DIFFRACTION99
2.7798-2.8550.32581590.2562716X-RAY DIFFRACTION100
2.855-2.9390.26811400.25412824X-RAY DIFFRACTION100
2.939-3.03380.29191470.24352711X-RAY DIFFRACTION100
3.0338-3.14230.34031330.24462781X-RAY DIFFRACTION100
3.1423-3.2680.31661290.23812815X-RAY DIFFRACTION100
3.268-3.41670.28491200.23112787X-RAY DIFFRACTION100
3.4167-3.59680.26571130.2112803X-RAY DIFFRACTION100
3.5968-3.82210.23361300.18932783X-RAY DIFFRACTION100
3.8221-4.11710.21751370.18562770X-RAY DIFFRACTION100
4.1171-4.53120.21891460.16382797X-RAY DIFFRACTION100
4.5312-5.18620.23281390.16512808X-RAY DIFFRACTION100
5.1862-6.53170.23781380.19082818X-RAY DIFFRACTION100
6.5317-49.63260.1911740.1672813X-RAY DIFFRACTION99

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more